I went thru the same thing last spring when I bought a new custom.

Since they fit me, and I had never dealt with hydraulic road brakes, I decided to have them source the parts and build it. It cost a bit more, but I wanted it built right the first time. If there were any issues, I could go back to them instead of having a pissing contest over whose fault it is.

I did supply a few pieces, like a Flite Ti seat, and pedals. I also drew the line at wheels. I wanted wheels with Shimano CX disc hubs, and Pacenti SL 25 rims. The shop quoted me ~$1000 which was absurd. ergott quoted me $650. I gave the shop a chance to match ergott and they said they couldn't move on the price at all., so ergott built them up (great wheels, BTW).

I ended up having issues with the rear brake. The free travel in the lever got to be too much after about a month. I brought the bike in 3 times before we left on our trip, and now that we're back, I'll have it checked again. After the third time, we were on our trip, and the hood was so stretched out, it wouldn't stay put. After dealing with it for about a month, I found a great shop in MN that cannibalized a hood from a bike on the floor.

Anyways, that's my story. I'm semi-ok at working on bikes and strip mine down every year, but I wanted the initial build done right. I was also a little short of time, too.

Good luck with the new bike!
Murph